BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy11095
(102 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3K5S|A Chain A, Crystal Structure Of Chicken T-Cadherin Ec1 Ec2
pdb|3K5S|B Chain B, Crystal Structure Of Chicken T-Cadherin Ec1 Ec2
Length = 217
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 42/88 (47%), Gaps = 1/88 (1%)
Query: 14 ADIKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQ-ETV 72
D+ V PLD E I Y L + V + + + + I + D ND P+F E V
Sbjct: 57 GDVSVTRPLDREAIANYQLEVEVTDLSGKIIDGPVRLDISVIDQNDNRPMFKEGPYVGHV 116
Query: 73 LEGEPIGSKVTQVNAIDKDGTFPNNQLL 100
+EG P G+ V ++ A D D +N LL
Sbjct: 117 MEGSPTGTTVMRMTAFDADDPSTDNALL 144
>pdb|3K5R|A Chain A, Crystal Structure Of Mouse T-Cadherin Ec1 Ec2
pdb|3K5R|B Chain B, Crystal Structure Of Mouse T-Cadherin Ec1 Ec2
Length = 218
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 14 ADIKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQ-ETV 72
+ V LD ETI Y L + + + L + +I+ D ND P+F E V
Sbjct: 58 GSVSVTRTLDRETIATYQLYVETTDASGKTLEGPVPLEVIVIDQNDNRPIFREGPYIGHV 117
Query: 73 LEGEPIGSKVTQVNAIDKDGTFPNNQLL 100
+EG P G+ V ++ A D D +N LL
Sbjct: 118 MEGSPTGTTVMRMTAFDADDPATDNALL 145
>pdb|3LNI|A Chain A, Crystal Structure Of E-Cadherin Ec12 E89a
pdb|3LNI|B Chain B, Crystal Structure Of E-Cadherin Ec12 E89a
Length = 213
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + +A + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVADPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|3Q2L|A Chain A, Mouse E-Cadherin Ec1-2 V81d Mutant
pdb|3Q2L|B Chain B, Mouse E-Cadherin Ec1-2 V81d Mutant
Length = 213
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L +++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHADSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|1EDH|A Chain A, E-Cadherin Domains 1 And 2 In Complex With Calcium
pdb|1EDH|B Chain B, E-Cadherin Domains 1 And 2 In Complex With Calcium
Length = 226
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 62 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 121
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 122 GAVPGTSVMKVSATDAD 138
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 22 LDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLF 64
LD E+ Y L ++ + + L++ A I ++D+ND P+F
Sbjct: 181 LDRESYPTYTLVVQAADLQGEGLSTTAKAVITVKDINDNAPVF 223
>pdb|1FF5|A Chain A, Structure Of E-Cadherin Double Domain
pdb|1FF5|B Chain B, Structure Of E-Cadherin Double Domain
Length = 219
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 61 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 120
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 121 GAVPGTSVMKVSATDAD 137
>pdb|3Q2V|A Chain A, Crystal Structure Of Mouse E-Cadherin Ectodomain
pdb|3Q2V|B Chain B, Crystal Structure Of Mouse E-Cadherin Ectodomain
Length = 550
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 33/71 (46%)
Query: 22 LDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQETVLEGEPIGSK 81
LD E+ Y L ++ + + L++ A I ++D+ND P+F + + + ++
Sbjct: 179 LDRESYPTYTLVVQAADLQGEGLSTTAKAVITVKDINDNAPVFNPSTYQGQVPENEVNAR 238
Query: 82 VTQVNAIDKDG 92
+ + D D
Sbjct: 239 IATLKVTDDDA 249
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGA--QQLASEATVHIILEDVNDEIPLFTEREQET-V 72
+K LD+E ++Y L +RVEN L + +E P+F E+ V
Sbjct: 282 LKTAKGLDFEAKQQYILHVRVENEEPFEGSLVPSTATVTVDVVDVNEAPIFMPAERRVEV 341
Query: 73 LEGEPIGSKVTQVNAIDKD 91
E +G ++T A + D
Sbjct: 342 PEDFGVGQEITSYTAREPD 360
>pdb|3LNG|A Chain A, Crystal Structure Of E-Cadherin Ec12 Aa Extension
pdb|3LNG|B Chain B, Crystal Structure Of E-Cadherin Ec12 Aa Extension
Length = 215
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 62 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 121
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 122 GAVPGTSVMKVSATDAD 138
>pdb|3LNE|A Chain A, Crystal Structure Of E-Cadherin Ec12 K14e
Length = 213
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|3QRB|A Chain A, Crystal Structure Of E-Cadherin Ec1-2 P5a P6a
pdb|3QRB|B Chain B, Crystal Structure Of E-Cadherin Ec1-2 P5a P6a
Length = 213
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|2QVF|B Chain B, Mouse E-cadherin Domains 1,2
Length = 213
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|1Q1P|A Chain A, E-Cadherin Activation
Length = 212
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 59 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 118
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 119 GAVPGTSVMKVSATDAD 135
>pdb|1SUH|A Chain A, Amino-Terminal Domain Of Epithelial Cadherin In The
Calcium Bound State, Nmr, 20 Structures
Length = 146
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 62 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 121
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 122 GAVPGTSVMKVSATDAD 138
>pdb|3LNH|A Chain A, Crystal Structure Of E-Cadherin Ec12 W2a
pdb|3LNH|B Chain B, Crystal Structure Of E-Cadherin Ec12 W2a
Length = 213
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|3Q2N|A Chain A, Mouse E-Cadherin Ec1-2 L175d Mutant
pdb|3Q2N|B Chain B, Mouse E-Cadherin Ec1-2 L175d Mutant
Length = 213
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|3LNF|A Chain A, Crystal Structure Of E-Cadherin Ec12 K14ew2a
pdb|3LNF|B Chain B, Crystal Structure Of E-Cadherin Ec12 K14ew2a
Length = 213
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQE-TVLE 74
+KV PLD E I +Y L ++ + + + I + D ND P FT+ E +V E
Sbjct: 60 LKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V+A D D
Sbjct: 120 GAVPGTSVMKVSATDAD 136
>pdb|2O72|A Chain A, Crystal Structure Analysis Of Human E-Cadherin (1-213)
Length = 213
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFT-EREQETVLE 74
+KV PLD E I Y L ++ + + I + D ND P FT E + +V+E
Sbjct: 60 LKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVME 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V +V A D D
Sbjct: 120 GALPGTSVMEVTATDAD 136
>pdb|4AQE|A Chain A, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2s70p And Protocadherin-15 Ec1-2 Form I
Length = 214
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 18 VNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQET-VLEGE 76
+ PLD ET E+ + V ++ Q V+I + DVND P F + + E
Sbjct: 67 LRQPLDRETKSEFTVEFSVSDH---QGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENT 123
Query: 77 PIGSKVTQVNAIDKD 91
P+G+ + VNA D D
Sbjct: 124 PVGTPIFIVNATDPD 138
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 59 DEIPLFTEREQETVL---EGEPIGSKVTQVNAIDKD 91
+ +P FT +T L E P+GS VTQ+ A D D
Sbjct: 4 NRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMD 39
>pdb|2WCP|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2
pdb|2WHV|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 (all Cation
Binding Sites Occupied By Calcium)
pdb|4APX|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form I
pdb|4AQ8|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AQ8|B Chain B, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AXW|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2, Form I 2.2a
Length = 214
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 18 VNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQET-VLEGE 76
+ PLD ET E+ + V ++ Q V+I + DVND P F + + E
Sbjct: 67 LRQPLDRETKSEFTVEFSVSDH---QGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENT 123
Query: 77 PIGSKVTQVNAIDKD 91
P+G+ + VNA D D
Sbjct: 124 PVGTPIFIVNATDPD 138
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 59 DEIPLFTEREQETVL---EGEPIGSKVTQVNAIDKD 91
+ +P FT +T L E P+GS VTQ+ A D D
Sbjct: 4 NRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMD 39
>pdb|3MVS|A Chain A, Structure Of The N-Terminus Of Cadherin 23
Length = 210
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 18 VNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQET-VLEGE 76
+ PLD ET E+ + V ++ Q V+I + DVND P F + + E
Sbjct: 66 LRQPLDRETKSEFTVEFSVSDH---QGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENT 122
Query: 77 PIGSKVTQVNAIDKD 91
P+G+ + VNA D D
Sbjct: 123 PVGTPIFIVNATDPD 137
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 16 IKVNHPLDYETIKEYNLTIRV-ENNGAQQLASEATVHIILEDVND 59
+ V LDYE + Y LT+ + + + L++ A + II+ D+ D
Sbjct: 164 VTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIITDMQD 208
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 60 EIPLFTEREQETVL---EGEPIGSKVTQVNAIDKD 91
+P FT +T L E P+GS VTQ+ A D D
Sbjct: 4 RLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMD 38
>pdb|1Q55|A Chain A, W-Shaped Trans Interactions Of Cadherins Model Based On
Fitting C- Cadherin (1l3w) To 3d Map Of Desmosomes
Obtained By Electron Tomography
pdb|1Q55|B Chain B, W-Shaped Trans Interactions Of Cadherins Model Based On
Fitting C- Cadherin (1l3w) To 3d Map Of Desmosomes
Obtained By Electron Tomography
pdb|1Q55|C Chain C, W-Shaped Trans Interactions Of Cadherins Model Based On
Fitting C- Cadherin (1l3w) To 3d Map Of Desmosomes
Obtained By Electron Tomography
pdb|1Q55|D Chain D, W-Shaped Trans Interactions Of Cadherins Model Based On
Fitting C- Cadherin (1l3w) To 3d Map Of Desmosomes
Obtained By Electron Tomography
pdb|1Q5A|A Chain A, S-Shaped Trans Interactions Of Cadherins Model Based On
Fitting C- Cadherin (1l3w) To 3d Map Of Desmosomes
Obtained By Electron Tomography
pdb|1Q5A|B Chain B, S-Shaped Trans Interactions Of Cadherins Model Based On
Fitting C- Cadherin (1l3w) To 3d Map Of Desmosomes
Obtained By Electron Tomography
pdb|1Q5B|A Chain A, Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
pdb|1Q5B|B Chain B, Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
pdb|1Q5B|C Chain C, Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
pdb|1Q5C|A Chain A, S-S-Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
pdb|1Q5C|B Chain B, S-S-Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
pdb|1Q5C|C Chain C, S-S-Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
pdb|1Q5C|D Chain D, S-S-Lambda-Shaped Trans And Cis Interactions Of Cadherins
Model Based On Fitting C-Cadherin (1l3w) To 3d Map Of
Desmosomes Obtained By Electron Tomography
Length = 880
Score = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%)
Query: 22 LDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQETVLEGEPIGSK 81
LD E EY LT++ + L+ E I + D ND P+F + ++ IG +
Sbjct: 334 LDREKFPEYTLTVQATDLEGAGLSVEGKAIIQITDANDNAPIFDPKTYTALVPENEIGFE 393
Query: 82 VTQVNAIDKD 91
V +++ D D
Sbjct: 394 VQRLSVTDLD 403
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 18 VNHPLDYETIKEYNLTIRV--ENNGAQQLASEATVHIILEDVNDEIPLFTERE-QETVLE 74
V PLD E +Y L+ EN + E T+++I D ND P FT+ + +V E
Sbjct: 217 VTRPLDREEYDKYVLSSHAVSENGSPVEEPMEITINVI--DQNDNRPKFTQDVFRGSVRE 274
Query: 75 GEPIGSKVTQVNAIDKD 91
G G++V V+A D+D
Sbjct: 275 GVQPGTQVMAVSATDED 291
>pdb|3Q2W|A Chain A, Crystal Structure Of Mouse N-Cadherin Ectodomain
Length = 559
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 30 YNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQETVLEGEPIGSKVTQVNAID 89
YN T +NG ++ T+ I L D+ND P +E ET EP +T A+D
Sbjct: 412 YNATFLASDNGIPPMSGTGTLQIYLLDINDNAPQVLPQEAETCETPEPNSINIT---ALD 468
Query: 90 KD 91
D
Sbjct: 469 YD 470
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 16 IKVNHPLDYETIKEYNLTIR---VENNGAQQLASEATVHIILEDVNDEIPLFT 65
I V LD E +++Y L I+ +E N L++ AT I + DVND P FT
Sbjct: 172 ITVAAGLDREKVQQYTLIIQATDMEGNPTYGLSNTATAVITVTDVNDNPPEFT 224
Score = 33.1 bits (74), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTERE-QETVLE 74
+ V PLD E I ++L + Q+ + + I + D+ND P F + +V E
Sbjct: 60 LSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRPEFLHQVWNGSVPE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V V AID D
Sbjct: 120 GSKPGTYVMTVTAIDAD 136
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 41/86 (47%), Gaps = 14/86 (16%)
Query: 16 IKVNHPLDYETIKEYNLTIRVEN-----NGAQQLA-SEATVHIILEDVNDEIPLFTER-- 67
+ V P+D+ET + + LT+ EN G Q S ATV + + DVN E P F
Sbjct: 285 VTVVKPIDFETNRMFVLTVAAENQVPLAKGIQHPPQSTATVSVTVIDVN-ENPYFAPNPK 343
Query: 68 --EQETVLEGEPIGSKVTQVNAIDKD 91
QE EG G+ +T + A D D
Sbjct: 344 IIRQE---EGLHAGTMLTTLTAQDPD 366
>pdb|1L3W|A Chain A, C-Cadherin Ectodomain
Length = 546
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%)
Query: 22 LDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQETVLEGEPIGSK 81
LD E EY LT++ + L+ E I + D ND P+F + ++ IG +
Sbjct: 185 LDREKFPEYTLTVQATDLEGAGLSVEGKAIIQITDANDNAPIFDPKTYTALVPENEIGFE 244
Query: 82 VTQVNAIDKD 91
V +++ D D
Sbjct: 245 VQRLSVTDLD 254
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 18 VNHPLDYETIKEYNLTIRV--ENNGAQQLASEATVHIILEDVNDEIPLFTERE-QETVLE 74
V PLD E +Y L+ EN + E T+++I D ND P FT+ + +V E
Sbjct: 68 VTRPLDREEYDKYVLSSHAVSENGSPVEEPMEITINVI--DQNDNRPKFTQDVFRGSVRE 125
Query: 75 GEPIGSKVTQVNAIDKD 91
G G++V V+A D+D
Sbjct: 126 GVQPGTQVMAVSATDED 142
>pdb|3PPE|A Chain A, Crystal Structure Of Chicken Ve-Cadherin Ec1-2
pdb|3PPE|B Chain B, Crystal Structure Of Chicken Ve-Cadherin Ec1-2
Length = 203
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 14 ADIKVNHPLDYETIKEYNLTIRV-ENNGAQQLASEATVHIILEDVNDEIPLFTER-EQET 71
DI LD E EY LT + + + L + I + D+ND P+F ++ +
Sbjct: 53 GDIYAFERLDREKKAEYELTAHIIDRRNNRSLEPPSKFIIKVSDINDNAPIFVQKIFNGS 112
Query: 72 VLEGEPIGSKVTQVNAIDKD 91
V E +G+ VT+V A D D
Sbjct: 113 VPEMSRLGTSVTKVTAEDAD 132
>pdb|2QVI|A Chain A, Crystal Structure Of N-Cadherin Domains Ec12
Length = 215
Score = 32.7 bits (73), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTERE-QETVLE 74
+ V PLD E I ++L + Q+ + + I + D+ND P F + +V E
Sbjct: 60 LSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRPEFLHQVWNGSVPE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V V AID D
Sbjct: 120 GSKPGTYVMTVTAIDAD 136
>pdb|1NCJ|A Chain A, N-Cadherin, Two-Domain Fragment
Length = 215
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTERE-QETVLE 74
+ V PLD E I ++L + Q+ + + I + D+ND P F + +V E
Sbjct: 60 LSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRPEFLHQVWNGSVPE 119
Query: 75 GEPIGSKVTQVNAIDKD 91
G G+ V V AID D
Sbjct: 120 GSKPGTYVMTVTAIDAD 136
>pdb|2WD0|A Chain A, Crystal Structure Of Nonsyndromic Deafness (Dfnb12)
Associated Mutant D124g Of Mouse Cadherin-23 Ec1-2
pdb|2WD0|C Chain C, Crystal Structure Of Nonsyndromic Deafness (Dfnb12)
Associated Mutant D124g Of Mouse Cadherin-23 Ec1-2
pdb|4AQA|A Chain A, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2d124g And Protocadherin-15 Ec1-2 Form I
Length = 214
Score = 32.3 bits (72), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 18 VNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQET-VLEGE 76
+ PLD ET E+ + V ++ Q V+I + VND P F + + E
Sbjct: 67 LRQPLDRETKSEFTVEFSVSDH---QGVITRKVNIQVGGVNDNAPTFHNQPYSVRIPENT 123
Query: 77 PIGSKVTQVNAIDKD 91
P+G+ + VNA D D
Sbjct: 124 PVGTPIFIVNATDPD 138
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 59 DEIPLFTEREQETVL---EGEPIGSKVTQVNAIDKD 91
+ +P FT +T L E P+GS VTQ+ A D D
Sbjct: 4 NRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMD 39
>pdb|3UBH|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-4
Length = 419
Score = 32.0 bits (71), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 8/82 (9%)
Query: 16 IKVNHPLDYETIKE---YNLTIRV-ENNGAQQLASEATVHIILEDVNDEIPLF--TEREQ 69
+K+ LD+E +++ Y+L + E++G + + T+ + DVND P F + +
Sbjct: 274 VKLAKELDFEDLRQPHVYSLIVTATEDSGGFSTSVDLTIRVT--DVNDNAPKFELPDYQA 331
Query: 70 ETVLEGEPIGSKVTQVNAIDKD 91
V E P+G+ + +V A+D D
Sbjct: 332 HNVDEDIPLGTSILRVKAMDSD 353
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 16 IKVNHPLDYE------TIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTERE- 68
++V DYE TI + + + +N + V I+++DVNDE P F R
Sbjct: 57 VRVKKKWDYEELGPEKTIDFWVIITNMGHNAGIKYTDNQRVIILVKDVNDEPPYFINRPL 116
Query: 69 --QETVLEGEPIGSKVTQVNAIDKD 91
Q V P + V + A D D
Sbjct: 117 PMQAVVQLNAPPNTPVFTLQARDPD 141
>pdb|3LND|A Chain A, Crystal Structure Of Cadherin-6 Ec12 W4a
pdb|3LND|B Chain B, Crystal Structure Of Cadherin-6 Ec12 W4a
pdb|3LND|C Chain C, Crystal Structure Of Cadherin-6 Ec12 W4a
pdb|3LND|D Chain D, Crystal Structure Of Cadherin-6 Ec12 W4a
Length = 207
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 14 ADIKVNHPLDYETIKEYNLTIR-VENNGAQQLASEATVHIILEDVNDEIPLFTER-EQET 71
DI+ LD E Y L + V + + E+ I + D+ND P+FT+ T
Sbjct: 55 GDIQATKRLDREEKPVYILRAQAVNRRTGRPVEPESEFIIKIHDINDNEPIFTKDVYTAT 114
Query: 72 VLEGEPIGSKVTQVNAIDKD 91
V E +G+ V QV A D D
Sbjct: 115 VPEMADVGTFVVQVTATDAD 134
>pdb|2EE0|A Chain A, Solution Structures Of The Ca Domain Of Human
Protocadherin 9
Length = 114
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 58 NDEIPLFTEREQET-VLEGEPIGSKVTQVNAIDKD 91
ND P+F E + E + E P+G+ V Q++A D D
Sbjct: 8 NDNRPVFKEGQVEVHIPENAPVGTSVIQLHATDAD 42
>pdb|2YST|A Chain A, Solution Structure Of The Third Cadherin Domain From Human
Protocadherin 7
Length = 119
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIP 62
+ V H +D E + + T+ + G +ATV + ++D ND +P
Sbjct: 73 LSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVP 119
>pdb|2A62|A Chain A, Crystal Structure Of Mouse Cadherin-8 Ec1-3
Length = 322
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 16 IKVNHPLDYETIKEYNLTIRVEN-------NGAQQLASEATVHIILE 55
I++ PLD+ET K Y L + N + ATV I++E
Sbjct: 276 IRLRKPLDFETKKSYTLKVEAANIHIDPRFSSRGPFKDTATVKIVVE 322
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 14 ADIKVNHP-LDYETIKEYNLTIRVENNGAQQ--LASEATVHIILEDVNDEIPLFTEREQE 70
A IK P +D E +EY + I+ ++ G L+ T+ + L DVND P F +
Sbjct: 162 AIIKTALPNMDREAKEEYLVVIQAKDMGGHSGGLSGTTTLTVTLTDVNDNPPKFAQSLYH 221
Query: 71 -TVLEGEPIGSKVTQVNAIDKD 91
+V E +G+ + +V A D+D
Sbjct: 222 FSVPEDVVLGTAIGRVKANDQD 243
>pdb|3UBF|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-3, I
pdb|3UBG|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-3, Ii
pdb|3UBG|B Chain B, Crystal Structure Of Drosophila N-Cadherin Ec1-3, Ii
Length = 316
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 16 IKVNHPLDYE------TIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTERE- 68
++V DYE TI + + + +N + V I+++DVNDE P F R
Sbjct: 52 VRVKKKWDYEELGPEKTIDFWVIITNMGHNAGIKYTDNQRVIILVKDVNDEPPYFINRPL 111
Query: 69 --QETVLEGEPIGSKVTQVNAIDKD 91
Q V P + V + A D D
Sbjct: 112 PMQAVVQLNAPPNTPVFTLQARDPD 136
>pdb|3OW2|D Chain D, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 165
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 7/50 (14%)
Query: 38 NNGAQQLASEATVHIILEDVNDEIPLFTEREQET----VLEGEPIGSKVT 83
+G + LA+ IL ++ ++P+ T+ ++ + EG+PIG+KVT
Sbjct: 19 GHGGRDLAN---AEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVT 65
>pdb|2WBX|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1
Length = 102
Score = 25.4 bits (54), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 59 DEIPLFTEREQETVL---EGEPIGSKVTQVNAIDKD 91
+ +P FT +T L E P+GS VTQ+ A D D
Sbjct: 4 NRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMD 39
>pdb|1FFK|D Chain D, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|G Chain G, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules
Are In The File 1gix
pdb|1JJ2|D Chain D, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|D Chain D, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|F Chain F, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|F Chain F, Co-Crystal Structure Of Tylosin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1KD1|F Chain F, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|F Chain F, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|F Chain F, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1ML5|GG Chain g, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1K73|F Chain F, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|F Chain F, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|F Chain F, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|F Chain F, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|F Chain F, Crystal Structure Of Ccdap-puromycin Bound At The
Peptidyl Transferase Center Of The 50s Ribosomal
Subunit
pdb|1Q81|F Chain F, Crystal Structure Of Minihelix With 3' Puromycin Bound
To A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|F Chain F, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|F Chain F, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|D Chain D, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|D Chain D, Structure Of Cca Oligonucleotide Bound To The Trna
Binding Sites Of The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1W2B|D Chain D, Trigger Factor Ribosome Binding Domain In Complex With
50s
pdb|1YL3|G Chain G, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|2B66|G Chain G, 50s Ribosomal Subunit From A Crystal Structure Of
Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome. This File Contains The 50s Subunit From A
Crystal Structure Of Release Factor Rf1, Trnas And Mrna
Bound To The Ribosome And Is Described In Remark 400
pdb|2B9N|G Chain G, 50s Ribosomal Subunit From A Crystal Structure Of
Release Factor Rf2, Trnas And Mrna Bound To The
Ribosome. This File Contains The 50s Subunit From A
Crystal Structure Of Release Factor Rf1, Trnas And Mrna
Bound To The Ribosome And Is Described In Remark 400.
pdb|2B9P|G Chain G, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex
With Trnas And Mrna With A Stop Codon In The A-Site And
Is Described In Remark 400.
pdb|3CXC|D Chain D, The Structure Of An Enhanced Oxazolidinone Inhibitor
Bound To The 50s Ribosomal Subunit Of H. Marismortui
Length = 176
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 7/50 (14%)
Query: 38 NNGAQQLASEATVHIILEDVNDEIPLFTEREQET----VLEGEPIGSKVT 83
+G + LA+ IL ++ ++P+ T+ ++ + EG+PIG+KVT
Sbjct: 28 GHGGRDLAN---AEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVT 74
>pdb|1S72|D Chain D, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|D Chain D, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|D Chain D, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|D Chain D, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|D Chain D, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|D Chain D, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|D Chain D, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|D Chain D, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|D Chain D, The Structure Of The Transition State Analogue "daa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ5|D Chain D, The Structure Of The Transition State Analogue "raa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ6|D Chain D, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|D Chain D, The Structure Of The Transition State Analogue "dca"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ8|D Chain D, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|D Chain D, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|D Chain D, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|D Chain D, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|D Chain D, The Structure Of The Transition State Analogue "dan"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQN|D Chain D, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|D Chain D, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|D Chain D, The Structure Of The Transition State Analogue "rap"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|2OTJ|D Chain D, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|D Chain D, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|D Chain D, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|D Chain D, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|D Chain D, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|D Chain D, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|D Chain D, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|D Chain D, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|D Chain D, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|D Chain D, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|D Chain D, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3G4S|D Chain D, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|D Chain D, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|D Chain D, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|D Chain D, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|D Chain D, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
The Large Ribosomal Subunit
pdb|4ADX|D Chain D, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 177
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 7/50 (14%)
Query: 38 NNGAQQLASEATVHIILEDVNDEIPLFTEREQET----VLEGEPIGSKVT 83
+G + LA+ IL ++ ++P+ T+ ++ + EG+PIG+KVT
Sbjct: 29 GHGGRDLAN---AEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVT 75
>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
Length = 525
Score = 25.4 bits (54), Expect = 8.6, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 9 LLFTWADIKVNHPLDYETIKEYNLTIRVENNGAQQLAS 46
L +W D K +PL +KE + T + N G Q + S
Sbjct: 363 LFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCS 400
>pdb|2IJG|X Chain X, Crystal Structure Of Cryptochrome 3 From Arabidopsis
Thaliana
pdb|2VTB|A Chain A, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|C Chain C, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|D Chain D, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|E Chain E, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|F Chain F, Structure Of Cryptochrome 3 - Dna Complex
Length = 526
Score = 25.4 bits (54), Expect = 8.6, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 9 LLFTWADIKVNHPLDYETIKEYNLTIRVENNGAQQLAS 46
L +W D K +PL +KE + T + N G Q + S
Sbjct: 363 LFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCS 400
>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
Length = 525
Score = 25.4 bits (54), Expect = 8.6, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 9 LLFTWADIKVNHPLDYETIKEYNLTIRVENNGAQQLAS 46
L +W D K +PL +KE + T + N G Q + S
Sbjct: 362 LFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCS 399
>pdb|2QKD|A Chain A, Crystal Structure Of Tandem Zpr1 Domains
Length = 404
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/47 (23%), Positives = 26/47 (55%)
Query: 29 EYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQETVLEG 75
Y LT+R + + +++ + + +++ EIP F+++ T +EG
Sbjct: 66 RYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEG 112
>pdb|1NP7|A Chain A, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
pdb|1NP7|B Chain B, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
Length = 489
Score = 25.4 bits (54), Expect = 9.3, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 13 WADIKVNHPLDYETIKEYNLTIRVENNGAQQLAS 46
W + +PL ++E NLT + N G Q +AS
Sbjct: 330 WRSGQTGYPLVDANMRELNLTGFMSNRGRQNVAS 363
>pdb|1Y4T|A Chain A, Ferric Binding Protein From Campylobacter Jejuni
pdb|1Y4T|D Chain D, Ferric Binding Protein From Campylobacter Jejuni
pdb|3E13|X Chain X, Iron Reconstituted Ferric Binding Protein From
Campylobacter Jejuni
Length = 322
Score = 25.4 bits (54), Expect = 9.4, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 23 DYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIPLFTEREQETVLEGEPIG 79
D+E IK++ ++ N Q ASE + LE N +F + + E + +G
Sbjct: 15 DFEIIKKFEEKTGIKVNHTQAKASELIKRLSLEGSNSPADIFITADISNLTEAKNLG 71
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,004,609
Number of Sequences: 62578
Number of extensions: 106536
Number of successful extensions: 261
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 199
Number of HSP's gapped (non-prelim): 71
length of query: 102
length of database: 14,973,337
effective HSP length: 67
effective length of query: 35
effective length of database: 10,780,611
effective search space: 377321385
effective search space used: 377321385
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)